Different z-stacks heights for each stage position
#1
In my experiments, I usually do time-lapses at different stage positions with rapid z-stack acquisitions (stream z function) for every time points. In order to avoid excessive illumination and phototoxicity, I am searching a way to acquire different z-stacks heights at each stage position. Example :

Timepoint 1 : 
  • Position 1 : zstack size : 40um ; step size 0.5um
  • Position 2 :  zstack size : 20um; step size 0.5um
  • Position 2 :  zstack size : 10um; step size 0.5um
  • ...
Timepoint 2 : 
  • Position 1 : zstack size : 40um ; step size 0.5um
  • Position 2 :  zstack size : 20um; step size 0.5um
  • Position 2 :  zstack size : 10um; step size 0.5um
  • ...
Any ideas how I could do that plz ?
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#2
Are you using Multi Dimensional Acquisition with the built in Z streaming or another function?
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#3
(11-30-2017, 06:45 AM)Neal.Gliksman Wrote: Are you using Multi Dimensional Acquisition with the built in Z streaming or another function?

Yes I am using MDA. From what I understand, I cannot run different zheights through MDA. I am trying now to run a journal where I can set the z height and the z step and use it with "use advanced stage position/wavelenght acquisition parameters.
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#4
The key will be using the variables MDA.ZSeries.Bottom, MDA.ZSeries.NumSteps, MDA.ZSeries.StepSize, and MDA.ZSeries.Top. I know all of the variables are writable, but I do not know the dependencies. What I mean by dependencies - if you change he NumSteps and StepSize does that automatically change the Top or Bottom?

Create journals for the different combinations you hope to have (10, 20, 40, ...). The journals are simply Assign Variables and maybe the only thing you need to change is MDA.ZSeries.NumSteps. Then assign the custom journals to the positions using the advanced stage position/wavelength table.
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